Had the same problem on 2 WP sites. Fixed the issue by restarting apache immediately after updating W3TC plugin - this cleared my APC cache. I'm using APC for PHP opcode, W3TC db/object caches. HTH.
Btw, 0.9.4 seems to have moved CloudFlare support to an "extension". I am no longer enabling CloudFlare from within W3TC, will manage it directly on cloudflare.com. Don't want to break my sites with future upgrades.